BIOL 1610 Unit 3 Exam Study Guide: DNA Replication, Cell Cycle, Genetics, and Gene Regulation

Comprehensive practice flashcards based on the BIOL 1610 Unit 3 Study Guide covering cell cycle regulation, mitosis, meiosis, Mendelian and sex-linked inheritance, complex traits, DNA replication mechanisms, and gene regulation.

What are the three main phases of the cell cycle and their functions?

1. Interphase: The cell grows, copies its organelles, and duplicates its DNA (divided into $G_1$, $S$, and $G_2$ phases).
2. Mitosis: The division of the nucleus and distribution of identical chromosomes into two daughter nuclei.
3. Cytokinesis: The physical division of the cytoplasm into two distinct daughter cells.

What are three essential biological roles of cell division?

1. Reproduction (asexual reproduction in single-celled organisms).
2. Growth and development (allowing a multicellular organism to develop from a single fertilized egg).
3. Tissue renewal and repair (replacing dead, worn-out, or damaged cells).

In this electron micrograph of a duplicated chromosome, what do the top and bottom arrows point to?

The top arrow points to a chromatid (one of two identical sister chromatids), and the bottom arrow points to the centromere (the constricted region joining the sister chromatids).

How does a somatic cell compare to a gamete in terms of chromosome number and examples in the human body?

A human somatic cell is diploid ($2n = 46$ chromosomes) and makes up body tissues (e.g., skin cells, muscle cells). A human gamete is haploid ($n = 23$ chromosomes) and is a specialized sex cell (sperm or egg).

What is another name for the centrosome, and what is its primary function in animal cell division?

The centrosome is also called the microtubule-organizing center (MTOC). Its function is to organize the microtubules of the mitotic spindle that separate chromosomes during mitosis.

What key events occur during each of the five stages of mitosis (prophase, prometaphase, metaphase, anaphase, and telophase)?

• Prophase: Chromatin condenses into visible chromosomes, and the mitotic spindle begins to assemble. • Prometaphase: The nuclear envelope breaks down, and spindle microtubules attach to kinetochores. • Metaphase: Chromosomes align along the metaphase plate in the center of the cell. • Anaphase: Sister chromatids separate and are pulled toward opposite poles of the cell. • Telophase: Nuclear envelopes reform around two new sets of chromosomes, chromosomes decondense, and spindle microtubules depolymerize.

How do prokaryotes divide, and what is the role of the origin of replication in this process?

Prokaryotes reproduce through binary fission. The single circular DNA chromosome begins replicating at a specific site called the origin of replication. As replication finishes, the two origins move to opposite poles, the cell elongates, and the plasma membrane pinches inward to divide the cell.

What are the three major cell cycle checkpoints and their specific functions?

1. $G_1$ checkpoint: Checks cell size, nutrient availability, growth factors, and DNA damage before committing to divide.
2. $G_2$ checkpoint: Ensures DNA replication is complete and checks for DNA damage before entering mitosis.
3. $M$ (Spindle) checkpoint: Verifies that all kinetochores are properly attached to spindle microtubules at metaphase before triggering anaphase.

What is the $G_0$ phase, and which human cell types remain in it throughout their lifespans?

The $G_0$ phase is a non-dividing, quiescent state entered by cells that do not receive the go-ahead signal at the $G_1$ checkpoint. Mature nerve cells (neurons) and skeletal muscle cells typically remain in $G_0$ permanently.

What are HeLa cells, what is their historical source, and why are they biologically unique?

HeLa cells are an immortal human cell line derived in 1951 from cervical cancer cells taken from Henrietta Lacks. They are unique because, unlike normal human somatic cells that stop dividing after a fixed number of divisions, HeLa cells continue to divide indefinitely in culture.

Based on the human karyotype shown in Figure B, what is the sex of this individual, and how many homologous pairs are present?

The individual is male because of the presence of one $X$ chromosome and one $Y$ chromosome ($XY$). There are $23$ pairs of homologous chromosomes ($22$ pairs of autosomes and $1$ pair of sex chromosomes).

How does the chemotherapy drug Taxol (paclitaxel) disrupt mitosis, and why is it effective against cancer cells?

Taxol binds to and stabilizes spindle microtubules, preventing them from depolymerizing. This freezes the mitotic spindle, arresting cells in mitosis and leading to cell death, which preferentially targets rapidly dividing cancer cells.

What are the primary functions of helicase, topoisomerase, single-strand binding proteins, primase, DNA polymerase III, DNA polymerase I, and ligase during DNA replication?

• Helicase: Unwinds and separates template DNA strands. • Topoisomerase: Relieves torsional strain and supercoiling ahead of the replication fork. • Single-strand binding proteins (SSBPs): Stabilize single-stranded template DNA. • Primase: Synthesizes short RNA primers. • DNA polymerase III: Synthesizes new complementary DNA strands in the $5' \rightarrow 3'$ direction. • DNA polymerase I: Removes RNA primers and replaces them with DNA nucleotides. • DNA ligase: Joins Okazaki fragments by sealing nicks in the sugar-phosphate backbone.

Identify the three main chemical components of the nucleotide shown, and describe what attaches at the $5'$ and $3'$ positions.

The three components are a phosphate group, a pentose sugar (deoxyribose), and a nitrogenous base. The $5'$ carbon is covalently attached to the phosphate group, while the $3'$ carbon has a free hydroxyl ($-OH$) group where subsequent nucleotides are added.

Why can DNA polymerase synthesize a new strand only in the $5' \rightarrow 3'$ direction?

DNA polymerases can only catalyze phosphodiester bond formation by attaching the $5'$ phosphate of an incoming deoxynucleotide triphosphate to the free $3'-OH$ group of an existing polynucleotide strand.

How did Meselson and Stahl create 'heavy' DNA, and what banding pattern supported semiconservative replication after one and two generations?

They cultured bacteria in medium containing the heavy isotope $^{15}N$, then transferred them to medium with light $^{14}N$. • Generation 1: A single intermediate hybrid band ($^{15}N\text{-}^{14}N$). • Generation 2: Two distinct bands—one intermediate hybrid band ($^{15}N\text{-}^{14}N$) and one light band ($^{14}N\text{-}^{14}N$).

Using the racecar analogy shown, contrast the normal functions of proto-oncogenes and tumor suppressor genes with their mutated states in cancer.

In normal cells, proto-oncogenes act as the gas pedal (promoting cell division) and tumor suppressor genes act as the brakes (inhibiting cell division). Mutations that convert a proto-oncogene into an oncogene provide 'too much gas' (hyperactive signaling), while inactivating mutations in tumor suppressor genes cause 'no brakes' (loss of division inhibition). Both contribute to cancer.

How do silent, missense, nonsense, and frameshift mutations differ in their effects on protein structure?

• Silent: A base substitution changes a codon into a synonymous codon that specifies the exact same amino acid; no change in protein sequence. • Missense: A base substitution changes a codon to specify a different amino acid. • Nonsense: A base substitution converts an amino acid codon into a premature stop codon ($UAA$, $UAG$, or $UGA$), truncating the protein. • Frameshift: An insertion or deletion of nucleotides not in multiples of three shifts the translational reading frame, altering all downstream codons.

What is the difference between germline and somatic mutations regarding inheritance and evolution?

Germline mutations occur in gametes (sperm or egg) and can be passed on to future generations, serving as raw material for natural selection and evolution. Somatic mutations occur in non-reproductive body cells, affect only that individual, and cannot be inherited by offspring.

What stage of cell division is shown in this diagram, and how does its chromosome arrangement differ from metaphase of mitosis?

This shows Metaphase I of meiosis. Homologous chromosome pairs (tetrads/bivalents) align side-by-side along the metaphase plate, whereas in metaphase of mitosis, individual duplicated chromosomes line up single file.

What are the three primary mechanisms of sexual reproduction that generate genetic diversity in offspring?

1. Independent assortment of chromosomes at Metaphase I ($2^n$ possible combinations, where $n$ is the haploid number).
2. Crossing over between non-sister chromatids of homologous chromosomes during Prophase I.
3. Random fertilization (any genetically unique sperm can fertilize any genetically unique egg).

If an organism has a diploid chromosome number of $2n = 72$, how many homologous pairs does it have, and how many chromosomes are in its gametes?

It has $36$ pairs of homologous chromosomes ($\frac{72}{2} = 36$), and its gametes contain $36$ chromosomes ($n = 36$).

State Mendel's Law of Segregation and Law of Independent Assortment.

• Law of Segregation: The two alleles for a heritable gene segregate during gamete formation such that each gamete carries only one allele for each gene. • Law of Independent Assortment: Two or more genes assort independently of one another during gamete formation, provided they are located on different chromosomes (or far apart on the same chromosome).

In the pedigree shown for albinism (solid shapes indicate albinism), is the trait dominant or recessive, and what are the genotypes of the parents in Generation 1?

Albinism is an autosomal recessive trait because unaffected parents produce affected offspring (it skips generations). The parents in Generation 1 must both be heterozygous carriers ($Aa$).

A man with blood type A and a woman with blood type B have a child with blood type O. What are the parents' genotypes and the expected phenotypic ratio of their future offspring?

The parents must both carry the recessive allele: the father is $I^Ai$ and the mother is $I^Bi$. Their offspring have a $1:1:1:1$ phenotypic ratio ($25\text{\%}$ type AB [$I^AI^B$], $25\text{\%}$ type A [$I^Ai$], $25\text{\%}$ type B [$I^Bi$], and $25\text{\%}$ type O [$ii$]).

What phenotypic and sex distribution results from Thomas Hunt Morgan's cross between a white-eyed female fly ($X^wX^w$) and a red-eyed male fly ($X^{w+}Y$)?

All female offspring have red eyes ($X^{w+}X^w$), and all male offspring have white eyes ($X^wY$). This result confirmed that the white-eye gene is located on the $X$ chromosome.

A testcross produces 721 gray/red, 751 black/purple, 49 gray/purple, and 45 black/red offspring. Using the recombination frequency formula, what is the RF between these two genes?

Total recombinant offspring = $49 + 45 = 94$. Total offspring = $721 + 751 + 49 + 45 = 1566$. $\text{RF} = \frac{94}{1566} \times 100\% ≈ 6.0\%$ (or $6.0\,\text{map units/cM}$).

What is nondisjunction, and what are the definitions of aneuploidy, monosomy, and trisomy?

• Nondisjunction: Failure of homologous chromosomes (in meiosis I) or sister chromatids (in meiosis II) to separate properly. • Aneuploidy: An abnormal number of chromosomes in a zygote. • Monosomy: Missing one chromosome from a homologous pair ($2n - 1$). • Trisomy: Having an extra copy of a chromosome ($2n + 1$).

In the reaction norm graphs shown, which graphs illustrate a genotype-by-environment ($G \times E$) interaction?

Graphs E and F illustrate a genotype-by-environment ($G \times E$) interaction because the reaction norm lines for Genotype A and Genotype B are not parallel, indicating that the genotypes respond differently to environmental change.

Define heritability ($h^2$) and explain the biological meaning of $h^2 = 1$ versus $h^2 = 0$.

Heritability ($h^2$) is the proportion of total phenotypic variation in a population that is attributable to genetic differences among individuals. • $h^2 = 1$: $100\%$ of phenotypic variation is due to genetic differences; environmental variation contributes nothing. • $h^2 = 0$: All phenotypic variation is caused by environmental differences; genetic variation contributes nothing.

How do histone acetylation and DNA methylation alter chromatin structure and affect eukaryotic gene expression?

• Histone acetylation: Attaches acetyl groups to basic amino acids on histone tails, loosening chromatin packaging into transcriptionally active euchromatin and promoting gene expression. • DNA methylation: Adds methyl groups directly to cytosine bases in DNA, condensing chromatin into transcriptionally inactive heterochromatin and silencing gene expression.

How does the lac operon function when lactose is present and glucose is absent?

Lactose is converted to allolactose (inducer), which binds to the LacI repressor protein, altering its conformation so it detaches from the operator. Because glucose is absent, cyclic AMP ($\text{cAMP}$) levels are high. $\text{cAMP}$ binds to CRP (CAP), and the active $\text{cAMP-CRP}$ complex binds to the promoter, strongly stimulating RNA polymerase binding and transcription of the operon genes.

What is RNA interference (RNAi), and at what molecular level does it silence gene expression?

RNA interference (RNAi) is a gene-silencing process where small non-coding RNAs (such as miRNAs or siRNAs) associate with protein complexes (RISC) to bind complementary sequences on specific target mRNAs. This results in either enzymatic cleavage/degradation of the mRNA or blockage of its translation, silencing the gene at the mRNA (post-transcriptional) level.